The Story : The crew of seaQuest are joined by a reluctant Captain Nathan Bridger and set off to investigate a distress call from an underwater colony, only to find it is a trap by a renegade sub under the command of Captain Marilyn Stark, who has a personal vendetta against the seaQuest.

The Story : Two miles beneath the surface, seaQuest explores one of the ocean's truly remarkable phenomena: steaming hot hydrothermal vents play host to an underwater forest of giant tube worms and other forms of life where none was thought possible. But when Darwin the dolphin becomes deathly ill, Captain Bridger is forced to choose between the mission at hand and the life of one of his crew.

The Story : When a preserved annexe of the Great Library of Alexandria is discovered, many nations send their fleets to lay claim to its treasures. The UEO orders Bridger to mediate the dispute and sends a team of ESP parapsychologists to help the negotiations.

The Story : The crew of seaQuest rescue a warden and his only prisoner from beneath the ice cap. The prisoner escapes and reveals that he holds a deadly toxin which will be released unless the crew does as he says, which is launching the seaQuest's missiles against the UEO.

The Story : The seaQuest discovers a group of children living in an old munitions facility on the sea floor and they must evacuate them before the structure collapses and unleashes a deadly explosion. Meanwhile, Lucas develops a crush on the teenage girl.

The Story : When Commander Ford and other crew members are contaminated with a deadly virus from a downed space station, Captain Bridger finds himself fighting against the clock and a government cover-up to save them.

The Story : A hurricane threatens to prevent the rescue of a French sightseeing submarine which is stuck in a freshwater sink hole and running out of oxygen. When a team from the seaQuest are forced to the surface they must rely on each other to survive the storm.

The Story : When a vital component of seaQuest's air conditioning fails and regular channels fail, Krieg relies on a black market source called The Regulator. When Darwin disappears the seaQuest must track down the renegade who is seeking the meaning of life.

The Story : Hitchcock goes into an underwater gold mining colony in order to investigate a distress signal and discovers that the original and rightful owner of the mine and his family are being held hostage by an outlaw and his thugs.

The Story : When Lucas visits a communications base populated by a group of young computer experts, a famous computer hacker, who now runs the Node, persuades Lucas to break into the World Bank and divert funds for humanitarian causes.

The Story : seaQuest is hurriedly dispatched to rescue a crew returning from a manned mission to Mars when their space capsule crash lands in the Atlantic Ocean, but the president of an militarised Asian federation wants them too for his own reasons.

The Story : When a top-secret UEO project shows the approach of a catastrophic volcanic eruption, the crew of seaQuest must convince treasure seekers on the island to abandon their lifelong search or face certain death.

The Story : A renegade sub is sinking whaling ships, which are in themselves illegal and against their moral judgement, the crew of seaQuest must stop the sub from its mission. Meanwhile, Krieg is on a mission of his own: to have a cheeseburger, despite red meat being outlawed.

The Story : Ford accidentally stumbles onto a colony of genetically altered humans, adapted by a scientist to live underwater. Meanwhile, Lucas heads to a party on land where he thinks Juliana is waiting for him.

The Story : A brand new power plant which is set to supply energy to the whole world goes wrong and there is a danger of the polar ice caps melting. Bridger decides he must sacrifice the seaQuest in order to save the world. Meanwhile, Lucas has a reunion of sorts with his father.